The goal of pmcbioc is to facilitate summary and analysis of PubMedCentral result sets. The PubMedCentral results are XML files containing article metadata, the body of the article, and end matter (citations, etc.). pmcbioc parses the XML to extract article metadata (title, year, author, keyword, reference PMID) to a database for quick access. pmcbioc also indexes the PubMedCentral XML file and provides facilities for rapidly querying the file.
Installation
Install the development version of pmcbioc from GitHub with:
# install.packages("devtools")
devtools::install_github("mtmorgan/pmcbioc")Use and example
See the introduction article for basic use, including parsing and indexing the PubMedCentral XML to a database for fast access to key data.
Some simple observations from Bioconductor citations downloaded on 2023-10-18 include:
- Publications grow exponentially, perhaps at a decreased rate after 2010.
- PLoS ONE, Scientific Reports and Nature Communications are the three most prominent venues for publications about Bioconductor.
- Authors mentioning Bioconductor are a little difficult to distinguish (shared surname and given names), but the most mentioning unambiguous author is ‘Quackenbush’. ‘Huber’ is the most mentioning Bioconductor leader.
- Common keywords emphasize gene expression, RNA-Seq, methylation, transcriptomics, epigenetics, etc.
- Publications on edgeR, DESeq2, limma, and the original Bioconductor book are cited by other publications mentioning Bioconductor.